From: Karl O. Pinc Date: Sun, 21 Oct 2018 19:09:22 +0000 (-0500) Subject: Initial commit with files from GMI_Pyramid project X-Git-Url: https://papio.biology.duke.edu/gitweb/?a=commitdiff_plain;h=bc635ed166e86960e92711924bb894e33b6442b9;p=pgwui_core Initial commit with files from GMI_Pyramid project --- bc635ed166e86960e92711924bb894e33b6442b9 diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 0000000..8c78251 --- /dev/null +++ b/.coveragerc @@ -0,0 +1,7 @@ +[run] +branch = True +source = + pgwui_core + +[report] +show_missing = True diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9076ccc --- /dev/null +++ b/.gitignore @@ -0,0 +1,11 @@ +__pycache__/ +.pytest_cache/ +.cache/ +.coverage/ +.tox/ +build/ +devel/ +dist/ +docs/build/ +README.html +src/pgwui_core.egg-info/ diff --git a/LICENSE.txt b/LICENSE.txt new file mode 100644 index 0000000..dba13ed --- /dev/null +++ b/LICENSE.txt @@ -0,0 +1,661 @@ + GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. By contrast, +our General Public Licenses are intended to guarantee your freedom to +share and change all versions of a program--to make sure it remains free +software for all its users. + + When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +them if you wish), that you receive source code or can get it if you +want it, that you can change the software or use pieces of it in new +free programs, and that you know you can do these things. + + Developers that use our General Public Licenses protect your rights +with two steps: (1) assert copyright on the software, and (2) offer +you this License which gives you legal permission to copy, distribute +and/or modify the software. + + A secondary benefit of defending all users' freedom is that +improvements made in alternate versions of the program, if they +receive widespread use, become available for other developers to +incorporate. Many developers of free software are heartened and +encouraged by the resulting cooperation. However, in the case of +software used on network servers, this result may fail to come about. +The GNU General Public License permits making a modified version and +letting the public access it on a server without ever releasing its +source code to the public. + + The GNU Affero General Public License is designed specifically to +ensure that, in such cases, the modified source code becomes available +to the community. It requires the operator of a network server to +provide the source code of the modified version running there to the +users of that server. Therefore, public use of a modified version, on +a publicly accessible server, gives the public access to the source +code of the modified version. + + An older license, called the Affero General Public License and +published by Affero, was designed to accomplish similar goals. This is +a different license, not a version of the Affero GPL, but Affero has +released a new version of the Affero GPL which permits relicensing under +this license. + + The precise terms and conditions for copying, distribution and +modification follow. + + TERMS AND CONDITIONS + + 0. Definitions. + + "This License" refers to version 3 of the GNU Affero General Public License. + + "Copyright" also means copyright-like laws that apply to other kinds of +works, such as semiconductor masks. + + "The Program" refers to any copyrightable work licensed under this +License. Each licensee is addressed as "you". "Licensees" and +"recipients" may be individuals or organizations. + + To "modify" a work means to copy from or adapt all or part of the work +in a fashion requiring copyright permission, other than the making of an +exact copy. The resulting work is called a "modified version" of the +earlier work or a work "based on" the earlier work. + + A "covered work" means either the unmodified Program or a work based +on the Program. + + To "propagate" a work means to do anything with it that, without +permission, would make you directly or secondarily liable for +infringement under applicable copyright law, except executing it on a +computer or modifying a private copy. Propagation includes copying, +distribution (with or without modification), making available to the +public, and in some countries other activities as well. + + To "convey" a work means any kind of propagation that enables other +parties to make or receive copies. Mere interaction with a user through +a computer network, with no transfer of a copy, is not conveying. + + An interactive user interface displays "Appropriate Legal Notices" +to the extent that it includes a convenient and prominently visible +feature that (1) displays an appropriate copyright notice, and (2) +tells the user that there is no warranty for the work (except to the +extent that warranties are provided), that licensees may convey the +work under this License, and how to view a copy of this License. If +the interface presents a list of user commands or options, such as a +menu, a prominent item in the list meets this criterion. + + 1. Source Code. + + The "source code" for a work means the preferred form of the work +for making modifications to it. "Object code" means any non-source +form of a work. + + A "Standard Interface" means an interface that either is an official +standard defined by a recognized standards body, or, in the case of +interfaces specified for a particular programming language, one that +is widely used among developers working in that language. + + The "System Libraries" of an executable work include anything, other +than the work as a whole, that (a) is included in the normal form of +packaging a Major Component, but which is not part of that Major +Component, and (b) serves only to enable use of the work with that +Major Component, or to implement a Standard Interface for which an +implementation is available to the public in source code form. A +"Major Component", in this context, means a major essential component +(kernel, window system, and so on) of the specific operating system +(if any) on which the executable work runs, or a compiler used to +produce the work, or an object code interpreter used to run it. + + The "Corresponding Source" for a work in object code form means all +the source code needed to generate, install, and (for an executable +work) run the object code and to modify the work, including scripts to +control those activities. However, it does not include the work's +System Libraries, or general-purpose tools or generally available free +programs which are used unmodified in performing those activities but +which are not part of the work. For example, Corresponding Source +includes interface definition files associated with source files for +the work, and the source code for shared libraries and dynamically +linked subprograms that the work is specifically designed to require, +such as by intimate data communication or control flow between those +subprograms and other parts of the work. + + The Corresponding Source need not include anything that users +can regenerate automatically from other parts of the Corresponding +Source. + + The Corresponding Source for a work in source code form is that +same work. + + 2. Basic Permissions. + + All rights granted under this License are granted for the term of +copyright on the Program, and are irrevocable provided the stated +conditions are met. This License explicitly affirms your unlimited +permission to run the unmodified Program. The output from running a +covered work is covered by this License only if the output, given its +content, constitutes a covered work. This License acknowledges your +rights of fair use or other equivalent, as provided by copyright law. + + You may make, run and propagate covered works that you do not +convey, without conditions so long as your license otherwise remains +in force. You may convey covered works to others for the sole purpose +of having them make modifications exclusively for you, or provide you +with facilities for running those works, provided that you comply with +the terms of this License in conveying all material for which you do +not control copyright. Those thus making or running the covered works +for you must do so exclusively on your behalf, under your direction +and control, on terms that prohibit them from making any copies of +your copyrighted material outside their relationship with you. + + Conveying under any other circumstances is permitted solely under +the conditions stated below. Sublicensing is not allowed; section 10 +makes it unnecessary. + + 3. Protecting Users' Legal Rights From Anti-Circumvention Law. + + No covered work shall be deemed part of an effective technological +measure under any applicable law fulfilling obligations under article +11 of the WIPO copyright treaty adopted on 20 December 1996, or +similar laws prohibiting or restricting circumvention of such +measures. + + When you convey a covered work, you waive any legal power to forbid +circumvention of technological measures to the extent such circumvention +is effected by exercising rights under this License with respect to +the covered work, and you disclaim any intention to limit operation or +modification of the work as a means of enforcing, against the work's +users, your or third parties' legal rights to forbid circumvention of +technological measures. + + 4. Conveying Verbatim Copies. + + You may convey verbatim copies of the Program's source code as you +receive it, in any medium, provided that you conspicuously and +appropriately publish on each copy an appropriate copyright notice; +keep intact all notices stating that this License and any +non-permissive terms added in accord with section 7 apply to the code; +keep intact all notices of the absence of any warranty; and give all +recipients a copy of this License along with the Program. + + You may charge any price or no price for each copy that you convey, +and you may offer support or warranty protection for a fee. + + 5. Conveying Modified Source Versions. + + You may convey a work based on the Program, or the modifications to +produce it from the Program, in the form of source code under the +terms of section 4, provided that you also meet all of these conditions: + + a) The work must carry prominent notices stating that you modified + it, and giving a relevant date. + + b) The work must carry prominent notices stating that it is + released under this License and any conditions added under section + 7. This requirement modifies the requirement in section 4 to + "keep intact all notices". + + c) You must license the entire work, as a whole, under this + License to anyone who comes into possession of a copy. This + License will therefore apply, along with any applicable section 7 + additional terms, to the whole of the work, and all its parts, + regardless of how they are packaged. This License gives no + permission to license the work in any other way, but it does not + invalidate such permission if you have separately received it. + + d) If the work has interactive user interfaces, each must display + Appropriate Legal Notices; however, if the Program has interactive + interfaces that do not display Appropriate Legal Notices, your + work need not make them do so. + + A compilation of a covered work with other separate and independent +works, which are not by their nature extensions of the covered work, +and which are not combined with it such as to form a larger program, +in or on a volume of a storage or distribution medium, is called an +"aggregate" if the compilation and its resulting copyright are not +used to limit the access or legal rights of the compilation's users +beyond what the individual works permit. Inclusion of a covered work +in an aggregate does not cause this License to apply to the other +parts of the aggregate. + + 6. Conveying Non-Source Forms. + + You may convey a covered work in object code form under the terms +of sections 4 and 5, provided that you also convey the +machine-readable Corresponding Source under the terms of this License, +in one of these ways: + + a) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by the + Corresponding Source fixed on a durable physical medium + customarily used for software interchange. + + b) Convey the object code in, or embodied in, a physical product + (including a physical distribution medium), accompanied by a + written offer, valid for at least three years and valid for as + long as you offer spare parts or customer support for that product + model, to give anyone who possesses the object code either (1) a + copy of the Corresponding Source for all the software in the + product that is covered by this License, on a durable physical + medium customarily used for software interchange, for a price no + more than your reasonable cost of physically performing this + conveying of source, or (2) access to copy the + Corresponding Source from a network server at no charge. + + c) Convey individual copies of the object code with a copy of the + written offer to provide the Corresponding Source. This + alternative is allowed only occasionally and noncommercially, and + only if you received the object code with such an offer, in accord + with subsection 6b. + + d) Convey the object code by offering access from a designated + place (gratis or for a charge), and offer equivalent access to the + Corresponding Source in the same way through the same place at no + further charge. You need not require recipients to copy the + Corresponding Source along with the object code. If the place to + copy the object code is a network server, the Corresponding Source + may be on a different server (operated by you or a third party) + that supports equivalent copying facilities, provided you maintain + clear directions next to the object code saying where to find the + Corresponding Source. Regardless of what server hosts the + Corresponding Source, you remain obligated to ensure that it is + available for as long as needed to satisfy these requirements. + + e) Convey the object code using peer-to-peer transmission, provided + you inform other peers where the object code and Corresponding + Source of the work are being offered to the general public at no + charge under subsection 6d. + + A separable portion of the object code, whose source code is excluded +from the Corresponding Source as a System Library, need not be +included in conveying the object code work. + + A "User Product" is either (1) a "consumer product", which means any +tangible personal property which is normally used for personal, family, +or household purposes, or (2) anything designed or sold for incorporation +into a dwelling. In determining whether a product is a consumer product, +doubtful cases shall be resolved in favor of coverage. For a particular +product received by a particular user, "normally used" refers to a +typical or common use of that class of product, regardless of the status +of the particular user or of the way in which the particular user +actually uses, or expects or is expected to use, the product. A product +is a consumer product regardless of whether the product has substantial +commercial, industrial or non-consumer uses, unless such uses represent +the only significant mode of use of the product. + + "Installation Information" for a User Product means any methods, +procedures, authorization keys, or other information required to install +and execute modified versions of a covered work in that User Product from +a modified version of its Corresponding Source. The information must +suffice to ensure that the continued functioning of the modified object +code is in no case prevented or interfered with solely because +modification has been made. + + If you convey an object code work under this section in, or with, or +specifically for use in, a User Product, and the conveying occurs as +part of a transaction in which the right of possession and use of the +User Product is transferred to the recipient in perpetuity or for a +fixed term (regardless of how the transaction is characterized), the +Corresponding Source conveyed under this section must be accompanied +by the Installation Information. But this requirement does not apply +if neither you nor any third party retains the ability to install +modified object code on the User Product (for example, the work has +been installed in ROM). + + The requirement to provide Installation Information does not include a +requirement to continue to provide support service, warranty, or updates +for a work that has been modified or installed by the recipient, or for +the User Product in which it has been modified or installed. Access to a +network may be denied when the modification itself materially and +adversely affects the operation of the network or violates the rules and +protocols for communication across the network. + + Corresponding Source conveyed, and Installation Information provided, +in accord with this section must be in a format that is publicly +documented (and with an implementation available to the public in +source code form), and must require no special password or key for +unpacking, reading or copying. + + 7. Additional Terms. + + "Additional permissions" are terms that supplement the terms of this +License by making exceptions from one or more of its conditions. +Additional permissions that are applicable to the entire Program shall +be treated as though they were included in this License, to the extent +that they are valid under applicable law. If additional permissions +apply only to part of the Program, that part may be used separately +under those permissions, but the entire Program remains governed by +this License without regard to the additional permissions. + + When you convey a copy of a covered work, you may at your option +remove any additional permissions from that copy, or from any part of +it. (Additional permissions may be written to require their own +removal in certain cases when you modify the work.) You may place +additional permissions on material, added by you to a covered work, +for which you have or can give appropriate copyright permission. + + Notwithstanding any other provision of this License, for material you +add to a covered work, you may (if authorized by the copyright holders of +that material) supplement the terms of this License with terms: + + a) Disclaiming warranty or limiting liability differently from the + terms of sections 15 and 16 of this License; or + + b) Requiring preservation of specified reasonable legal notices or + author attributions in that material or in the Appropriate Legal + Notices displayed by works containing it; or + + c) Prohibiting misrepresentation of the origin of that material, or + requiring that modified versions of such material be marked in + reasonable ways as different from the original version; or + + d) Limiting the use for publicity purposes of names of licensors or + authors of the material; or + + e) Declining to grant rights under trademark law for use of some + trade names, trademarks, or service marks; or + + f) Requiring indemnification of licensors and authors of that + material by anyone who conveys the material (or modified versions of + it) with contractual assumptions of liability to the recipient, for + any liability that these contractual assumptions directly impose on + those licensors and authors. + + All other non-permissive additional terms are considered "further +restrictions" within the meaning of section 10. If the Program as you +received it, or any part of it, contains a notice stating that it is +governed by this License along with a term that is a further +restriction, you may remove that term. If a license document contains +a further restriction but permits relicensing or conveying under this +License, you may add to a covered work material governed by the terms +of that license document, provided that the further restriction does +not survive such relicensing or conveying. + + If you add terms to a covered work in accord with this section, you +must place, in the relevant source files, a statement of the +additional terms that apply to those files, or a notice indicating +where to find the applicable terms. + + Additional terms, permissive or non-permissive, may be stated in the +form of a separately written license, or stated as exceptions; +the above requirements apply either way. + + 8. Termination. + + You may not propagate or modify a covered work except as expressly +provided under this License. Any attempt otherwise to propagate or +modify it is void, and will automatically terminate your rights under +this License (including any patent licenses granted under the third +paragraph of section 11). + + However, if you cease all violation of this License, then your +license from a particular copyright holder is reinstated (a) +provisionally, unless and until the copyright holder explicitly and +finally terminates your license, and (b) permanently, if the copyright +holder fails to notify you of the violation by some reasonable means +prior to 60 days after the cessation. + + Moreover, your license from a particular copyright holder is +reinstated permanently if the copyright holder notifies you of the +violation by some reasonable means, this is the first time you have +received notice of violation of this License (for any work) from that +copyright holder, and you cure the violation prior to 30 days after +your receipt of the notice. + + Termination of your rights under this section does not terminate the +licenses of parties who have received copies or rights from you under +this License. If your rights have been terminated and not permanently +reinstated, you do not qualify to receive new licenses for the same +material under section 10. + + 9. Acceptance Not Required for Having Copies. + + You are not required to accept this License in order to receive or +run a copy of the Program. Ancillary propagation of a covered work +occurring solely as a consequence of using peer-to-peer transmission +to receive a copy likewise does not require acceptance. However, +nothing other than this License grants you permission to propagate or +modify any covered work. These actions infringe copyright if you do +not accept this License. Therefore, by modifying or propagating a +covered work, you indicate your acceptance of this License to do so. + + 10. Automatic Licensing of Downstream Recipients. + + Each time you convey a covered work, the recipient automatically +receives a license from the original licensors, to run, modify and +propagate that work, subject to this License. You are not responsible +for enforcing compliance by third parties with this License. + + An "entity transaction" is a transaction transferring control of an +organization, or substantially all assets of one, or subdividing an +organization, or merging organizations. If propagation of a covered +work results from an entity transaction, each party to that +transaction who receives a copy of the work also receives whatever +licenses to the work the party's predecessor in interest had or could +give under the previous paragraph, plus a right to possession of the +Corresponding Source of the work from the predecessor in interest, if +the predecessor has it or can get it with reasonable efforts. + + You may not impose any further restrictions on the exercise of the +rights granted or affirmed under this License. For example, you may +not impose a license fee, royalty, or other charge for exercise of +rights granted under this License, and you may not initiate litigation +(including a cross-claim or counterclaim in a lawsuit) alleging that +any patent claim is infringed by making, using, selling, offering for +sale, or importing the Program or any portion of it. + + 11. Patents. + + A "contributor" is a copyright holder who authorizes use under this +License of the Program or a work on which the Program is based. The +work thus licensed is called the contributor's "contributor version". + + A contributor's "essential patent claims" are all patent claims +owned or controlled by the contributor, whether already acquired or +hereafter acquired, that would be infringed by some manner, permitted +by this License, of making, using, or selling its contributor version, +but do not include claims that would be infringed only as a +consequence of further modification of the contributor version. For +purposes of this definition, "control" includes the right to grant +patent sublicenses in a manner consistent with the requirements of +this License. + + Each contributor grants you a non-exclusive, worldwide, royalty-free +patent license under the contributor's essential patent claims, to +make, use, sell, offer for sale, import and otherwise run, modify and +propagate the contents of its contributor version. + + In the following three paragraphs, a "patent license" is any express +agreement or commitment, however denominated, not to enforce a patent +(such as an express permission to practice a patent or covenant not to +sue for patent infringement). To "grant" such a patent license to a +party means to make such an agreement or commitment not to enforce a +patent against the party. + + If you convey a covered work, knowingly relying on a patent license, +and the Corresponding Source of the work is not available for anyone +to copy, free of charge and under the terms of this License, through a +publicly available network server or other readily accessible means, +then you must either (1) cause the Corresponding Source to be so +available, or (2) arrange to deprive yourself of the benefit of the +patent license for this particular work, or (3) arrange, in a manner +consistent with the requirements of this License, to extend the patent +license to downstream recipients. "Knowingly relying" means you have +actual knowledge that, but for the patent license, your conveying the +covered work in a country, or your recipient's use of the covered work +in a country, would infringe one or more identifiable patents in that +country that you have reason to believe are valid. + + If, pursuant to or in connection with a single transaction or +arrangement, you convey, or propagate by procuring conveyance of, a +covered work, and grant a patent license to some of the parties +receiving the covered work authorizing them to use, propagate, modify +or convey a specific copy of the covered work, then the patent license +you grant is automatically extended to all recipients of the covered +work and works based on it. + + A patent license is "discriminatory" if it does not include within +the scope of its coverage, prohibits the exercise of, or is +conditioned on the non-exercise of one or more of the rights that are +specifically granted under this License. You may not convey a covered +work if you are a party to an arrangement with a third party that is +in the business of distributing software, under which you make payment +to the third party based on the extent of your activity of conveying +the work, and under which the third party grants, to any of the +parties who would receive the covered work from you, a discriminatory +patent license (a) in connection with copies of the covered work +conveyed by you (or copies made from those copies), or (b) primarily +for and in connection with specific products or compilations that +contain the covered work, unless you entered into that arrangement, +or that patent license was granted, prior to 28 March 2007. + + Nothing in this License shall be construed as excluding or limiting +any implied license or other defenses to infringement that may +otherwise be available to you under applicable patent law. + + 12. No Surrender of Others' Freedom. + + If conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot convey a +covered work so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you may +not convey it at all. For example, if you agree to terms that obligate you +to collect a royalty for further conveying from those to whom you convey +the Program, the only way you could satisfy both those terms and this +License would be to refrain entirely from conveying the Program. + + 13. Remote Network Interaction; Use with the GNU General Public License. + + Notwithstanding any other provision of this License, if you modify the +Program, your modified version must prominently offer all users +interacting with it remotely through a computer network (if your version +supports such interaction) an opportunity to receive the Corresponding +Source of your version by providing access to the Corresponding Source +from a network server at no charge, through some standard or customary +means of facilitating copying of software. This Corresponding Source +shall include the Corresponding Source for any work covered by version 3 +of the GNU General Public License that is incorporated pursuant to the +following paragraph. + + Notwithstanding any other provision of this License, you have +permission to link or combine any covered work with a work licensed +under version 3 of the GNU General Public License into a single +combined work, and to convey the resulting work. The terms of this +License will continue to apply to the part which is the covered work, +but the work with which it is combined will remain governed by version +3 of the GNU General Public License. + + 14. Revised Versions of this License. + + The Free Software Foundation may publish revised and/or new versions of +the GNU Affero General Public License from time to time. Such new versions +will be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + + Each version is given a distinguishing version number. If the +Program specifies that a certain numbered version of the GNU Affero General +Public License "or any later version" applies to it, you have the +option of following the terms and conditions either of that numbered +version or of any later version published by the Free Software +Foundation. If the Program does not specify a version number of the +GNU Affero General Public License, you may choose any version ever published +by the Free Software Foundation. + + If the Program specifies that a proxy can decide which future +versions of the GNU Affero General Public License can be used, that proxy's +public statement of acceptance of a version permanently authorizes you +to choose that version for the Program. + + Later license versions may give you additional or different +permissions. However, no additional obligations are imposed on any +author or copyright holder as a result of your choosing to follow a +later version. + + 15. Disclaimer of Warranty. + + THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY +APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT +HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY +OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, +THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR +PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM +IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF +ALL NECESSARY SERVICING, REPAIR OR CORRECTION. + + 16. Limitation of Liability. + + IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS +THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY +GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE +USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF +DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD +PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), +EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF +SUCH DAMAGES. + + 17. Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + + Copyright (C) + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see . + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +. diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..9992bc9 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,10 @@ +recursive-include docs *.py +recursive-include docs *.rst +recursive-include docs Makefile +recursive-include tests *.py +include .coveragerc +include LICENSE.txt +include Makefile +include src/pgwui_core/VERSION +include tests/README +include tox.ini diff --git a/Makefile b/Makefile new file mode 100644 index 0000000..fc4e9ed --- /dev/null +++ b/Makefile @@ -0,0 +1,180 @@ +# Copyright (C) 2016, 2017, 2018 The Meme Factory, Inc. http://www.meme.com/ + +# This file is part of PGWUI_Core. +# +# This program is free software: you can redistribute it and/or +# modify it under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of +# the License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public +# License along with this program. If not, see +# . +# + +# Karl O. Pinc + +# This works on debian... +PYTHON_EXE=python3 +VIRTUALENV=virtualenv -p ${PYTHON_EXE} + +TARGETS = +EXTRA_TARGETS = README.html +SETUPTOOLS_STUFF = build dist src/pgwui_core.egg-info +PYTEST_STUFF = .cache tests/__pycache__ tests/.pytest_cache +COVERAGE_STUFF = .coverage +TOX_STUFF = .tox + +all: ${TARGETS} + +help: + @echo + @echo 'Usage: make TARGET' + @echo + @echo 'TARGET is one of:' + @echo 'README.html Make html version of README.rst' + @echo 'publish Update all public-facing info' + @echo ' ("check-manifest" + "upload" + "push")' + @echo 'run_tests Run regression tests' + @echo 'dist Create sdist Python package in ./dist' + @echo 'clean Removed generated data' + @echo + @echo 'Less used TARGETS are:' + @echo 'register_test Register project at pypi test site' + @echo 'register Register project at pypi live site' + @echo 'upload_test Upload project to pypi test site' + @echo 'upload Upload project to pypi live site' + @echo 'push Push repo changes to public repo' + @echo ' (Hooks at bitbucket update readthedocs)' + @echo 'check Quick run of regression tests,' + @echo 'pudb Run the python pudb debugger' + @echo ' only with the default python' + @echo 'devel/check-manifest' + @echo ' Create a check-manifest venv' + @echo 'check-manifest Run check-manifest' + @echo 'update_check-manifest' + @echo ' Upgrade check-manifest venv to latest' + @echo ' versions' + @echo + @echo 'This Makefile does not work with the docs. See:' + @echo 'cd docs; make help' + +README.html: README.rst + rst2html --strict README.rst > README.html + + +# Useless targets +# Register with pypi. +.PHONY: register_test +register_test: + python setup.py register -r https://testpypi.python.org/pypi + +.PHONY: register +register: + python setup.py register + + +# Not so useless targets, used by the package owners for package management +.PHONY: upload_test +upload_test: + python setup.py sdist upload -r https://testpypi.python.org/pypi + +.PHONY: upload +upload: + python setup.py sdist upload + +.PHONY: push + git push + +.PHONY: publish +publish: check-manifest upload push + + +# Development related targets + +# Re-create development environment when setup.py changes +devel: setup.py + rm -rf devel + mkdir devel + +devel/check-manifest: devel + [ -d devel/check-manifest ] \ + || ( ${VIRTUALENV} devel/check-manifest ; \ + devel/check-manifest/bin/pip install --upgrade pip ; \ + devel/check-manifest/bin/pip install --upgrade setuptools ; \ + devel/check-manifest/bin/pip install check-manifest ) + +update_check-manifest: devel/check-manifest + devel/check-manifest/bin/pip -U + +check-manifest: devel/check-manifest + devel/check-manifest/bin/check-manifest + +devel/testenv: devel + [ -d devel/testenv ] \ + || ( ${VIRTUALENV} devel/testenv ; \ + devel/testenv/bin/pip install --upgrade pip ; \ + devel/testenv/bin/pip install --upgrade setuptools ; \ + devel/testenv/bin/pip install tox) + +update_testenv: devel/testenv + devel/testenv/bin/pip -U + +.PHONY: run_tests +run_tests: devel/testenv + devel/testenv/bin/tox --skip-missing-interpreters + +.PHONY: dist +dist: + rm -rf dist + python setup.py sdist + +devel/pytest: devel dist + if [ ! -d devel/pytest ] ; then \ + ( ${VIRTUALENV} devel/pytest ; \ + devel/pytest/bin/pip install --upgrade pip ; \ + devel/pytest/bin/pip install --upgrade setuptools ; \ + devel/pytest/bin/pip install --upgrade wheel ; \ + devel/pytest/bin/pip install dist/pgwui_core-*.tar.gz ; \ + devel/pytest/bin/pip install flake8 ; \ + devel/pytest/bin/pip install pytest-cov ; ) \ + else \ + ( devel/pytest/bin/pip uninstall -y pgwui_core ; \ + devel/pytest/bin/pip install dist/pgwui_core-*.tar.gz ) ; \ + fi + +.PHONY: check +check: devel/pytest + devel/pytest/bin/flake8 . + devel/pytest/bin/py.test --cov=pgwui_core tests + +devel/pudb: devel dist + if [ ! -d devel/pudb ] ; then \ + ( ${VIRTUALENV} devel/pudb ; \ + devel/pudb/bin/pip install --upgrade pip ; \ + devel/pudb/bin/pip install --upgrade setuptools ; \ + devel/pytest/bin/pip install --upgrade wheel ; \ + devel/pudb/bin/pip install dist/pgwui_core-*.tar.gz ; \ + devel/pudb/bin/pip install pudb ; ) \ + else \ + ( devel/pudb/bin/pip uninstall -y pgwui_core ; \ + devel/pudb/bin/pip install dist/pgwui_core-*.tar.gz ) ; \ + fi + +.PHONY: pudb +pudb: devel/pudb + # echo 'import pudb; pu.db' | devel/pudb/bin/python + devel/pudb/bin/python + + +# Expected targets +.PHONY: clean +clean: + #$(MAKE) -C docs clean + rm -rf ${TARGETS} ${EXTRA_TARGETS} ${SETUPTOOLS_STUFF} \ + ${PYTEST_STUFF} ${COVERAGE_STUFF} ${TOX_STUFF} devel diff --git a/README.rst b/README.rst new file mode 100644 index 0000000..5bf6ab2 --- /dev/null +++ b/README.rst @@ -0,0 +1,93 @@ +.. Copyright (C) 2018 The Meme Factory, Inc. http://www.meme.com/ + + + This file is part of PGWUI_Core. + + This program is free software: you can redistribute it and/or + modify it under the terms of the GNU Affero General Public License + as published by the Free Software Foundation, either version 3 of + the License, or (at your option) any later version. + + This program is distributed in the hope that it will be useful, but + WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU + Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public + License along with this program. If not, see + . + + Karl O. Pinc + +.. #End Of Copyright Marker# + +PGWUI_Core +========= + +Short Documentation +------------------- + +PGWUI_Core stands for `PostgreSQL`_ Web User Interface Core. + +A Python framework for creating `PostgreSQL`_ web user interfaces. The +focus is on interfaces supporting bulk data upload or download, on +execution of batches of arbitrary SQL, and on transactions. A +distinguishing feature is an emphasis on discovering and reporting as +many errors as is possible per bulk interaction with the database. + +PGWUI_Core is a framework based on the `Pyramid`_ framework. It +provides modular and extendable capabilities, allowing you to +concentrate on the specific needs of your application. The +capabilities it provides include:: + + * Extendable web forms with fields supporting designation of + database and credentials. These forms are rendered using + `Pyramid`_ views. + + * Database connection objects which execute batches of SQL and + provide transaction support. + + * Database SQL handler objects responsible for mediating between the + application data and the database. This includes data validation, + pre-processing data received from the application, getting data + into and out of the database, and post-processing after the + database has finished executing the SQL. + + A distinguishing feature of PGWUI_Core is that database handler + objects can continue to execute statements within the current + transaction even after a statement has failed and it is known that + the transaction will roll back. This allows the reporting of + multiple errors per execution of a batch of SQL, while retaining + the all-or-nothing data modification property which transactions + provide. + + +Development Status +------------------ + +Although in use in production systems PGWUI_Core must be considered +Alpha code. This is because it is barely documented and barely has a +regression test suite. There is a reasonable likelihood that the API +will undergo some change before final Production release. Install a +specific version of PGWUI_Core to ensure a backwards incompatible +change does not break your code. + + +Complete Documentation +---------------------- + +The complete documentation set can be found on the PGWUI_Core home page at +http://pgwui_core.readthedocs.io/. + + +License +------- + +Except for files otherwise marked, distributed WITHOUT ANY WARRANTY +under the terms of the GNU Affero General Public License, version 3 or +a later version at your option. See the copyright notices at the top +of each file and the LICENSE.txt file for details. + + +.. _PostgreSQL: https://www.postgresql.org/ +.. _Pyramid: https://trypyramid.com/ diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..24eff81 --- /dev/null +++ b/setup.cfg @@ -0,0 +1,3 @@ +[bdist_wheel] +# Work with both python 2 and 3. +universal=1 diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..66fb75e --- /dev/null +++ b/setup.py @@ -0,0 +1,170 @@ +"""A setuptools based setup module. + +Copied from: +https://github.com/pypa/sampleproject +It's license applies to this file. +""" +# Copyright (c) 2016 The Python Packaging Authority (PyPA) +# +# Permission is hereby granted, free of charge, to any person obtaining a +# copy of this software and associated documentation files (the "Software"), +# to deal in the Software without restriction, including without limitation +# the rights to use, copy, modify, merge, publish, distribute, sublicense, +# and/or sell copies of the Software, and to permit persons to whom the +# Software is furnished to do so, subject to the following conditions: +# +# The above copyright notice and this permission notice shall be included in +# all copies or substantial portions of the Software. +# +# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING +# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER +# DEALINGS IN THE SOFTWARE. + + +# Always prefer setuptools over distutils +from setuptools import setup, find_packages +# To use a consistent encoding +from codecs import open +from os import path + + +# Get the long description from the README file +def filter_readme(): + '''Return README content with copyright at top removed''' + lines = [] + past_copyright = False + with open(path.join(here, 'README.rst'), encoding='utf-8') as f: + for line in f: + if past_copyright: + lines.append(line) + else: + if line == '.. #End Of Copyright Marker#\n': + past_copyright = True + return ''.join(lines) + + +here = path.abspath(path.dirname(__file__)) + +# Get program version +with open(path.join(here, 'src', 'pgwui_core', 'VERSION'), + encoding='utf-8') as version_file: + version = version_file.read().strip() + +# Get the long description from the README file +long_description = filter_readme() + +setup( + name='pgwui_core', + + # Versioning is major.minor.fixes. Major releases change (after 1.0.0) + # when backward incompatibility is introduced. Minor releases introduce + # new features. Fix releases introduce fixes. + version=version, + + description='A framework for creating PostgreSQL web user interfaces.', + long_description=long_description, + + # The project's main homepage. + url='http://pgwui_core.readthedocs.io/', + + # Author details + author='Karl O. Pinc', + author_email='kop@meme.com', + + # Choose your license + license='AGPLv3+', + + # See https://pypi.python.org/pypi?%3Aaction=list_classifiers + classifiers=[ + # How mature is this project? Common values are + # 3 - Alpha + # 4 - Beta + # 5 - Production/Stable + 'Development Status :: 3 - Alpha', + + # Indicate who your project is intended for + 'Intended Audience :: Developers', + 'Environment :: Web Environment', + 'Framework :: Pyramid', + 'Topic :: Database', + 'Topic :: Internet :: WWW/HTTP', + 'Topic :: Software Development :: Libraries :: Application Frameworks', + 'Topic :: Software Development :: User Interfaces', + + # Pick your license as you wish (should match "license" above) + ('License :: OSI Approved ' + ':: GNU Affero General Public License v3 or later (GPLv3+)'), + + # Specify the Python versions you support here. In particular, ensure + # that you indicate whether you support Python 2, Python 3 or both. + 'Programming Language :: Python :: 3', + 'Programming Language :: Python :: 3.4', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + ], + + # What does your project relate to? + keywords=( + 'batch', + 'batch upload', + 'bulk', + 'bulk data upload', + 'bulk upload', + 'bulk Postgres upload', + 'data upload', + 'error reporting', + 'library', + 'Postgres', + 'PostgreSQL', + 'psycopg2', + 'Pyramid', + 'software development', + 'SQL', + 'SQL execution', + 'transaction', + 'upload', + 'user interface', + 'web', + 'web development', + 'web framework', + 'web user interface', + ), + + # You can just specify the packages manually here if your project is + # simple. Or you can use find_packages(). + packages=find_packages('src'), + package_dir={'': 'src'}, + + # Run-time dependencies. + install_requires=[], + + # List additional groups of dependencies here (e.g. development + # dependencies). You can install these using the following syntax, + # for example: + # $ pip install -e .[dev,test] + # extras_require={ + # 'dev': ['check-manifest'], + # 'test': ['coverage'], + # }, + + # If there are data files included in your packages that need to be + # installed, specify them here. If using Python 2.6 or less, then these + # have to be included in MANIFEST.in as well. + package_data={ + 'pgwui_core': ['VERSION'], + }, + + # To provide executable scripts, use entry points in preference to the + # "scripts" keyword. Entry points provide cross-platform support and allow + # pip to create the appropriate form of executable for the target platform. + # entry_points={ + # 'console_scripts': [ + # 'sample=sample:main', + # ], + # }, +) diff --git a/src/pgwui_core/VERSION b/src/pgwui_core/VERSION new file mode 100644 index 0000000..77d6f4c --- /dev/null +++ b/src/pgwui_core/VERSION @@ -0,0 +1 @@ +0.0.0 diff --git a/src/pgwui_core/__init__.py b/src/pgwui_core/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/src/pgwui_core/form_constants.py b/src/pgwui_core/form_constants.py new file mode 100644 index 0000000..13840da --- /dev/null +++ b/src/pgwui_core/form_constants.py @@ -0,0 +1,37 @@ +# Copyright (C) 2013, 2014, 2018 The Meme Factory, Inc. http://www.meme.com/ + +# This file is part of PGWUI_Core. +# +# This program is free software: you can redistribute it and/or +# modify it under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of +# the License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public +# License along with this program. If not, see +# . + +# Karl O. Pinc +# + +# Constants used by the GMI pyramid programs. + +# The various important containers. +LIVE_DB = 'gombemi' +TEST_DB = 'gombemi_test' +DEFAULT_SCHEMA = 'gombemi' + +CSV = 'csv' +TAB = 'tab' + +# HTML radio button attributes +# (That these exist is a sign that we're not really utilizing our toolset.) +CSV_VALUE = CSV +TAB_VALUE = TAB +CHECKED = 'checked="checked"' +UNCHECKED = '' diff --git a/src/pgwui_core/pgwui_core.py b/src/pgwui_core/pgwui_core.py new file mode 100644 index 0000000..0836211 --- /dev/null +++ b/src/pgwui_core/pgwui_core.py @@ -0,0 +1,1940 @@ +# Copyright (C) 2018 The Meme Factory, Inc. http://www.meme.com/ + +# This file is part of PGWUI_Core. +# +# This program is free software: you can redistribute it and/or +# modify it under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of +# the License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public +# License along with this program. If not, see +# . +# + +# Karl O. Pinc + +'''Python source code for pgwui_core module + +More general description of the module. +''' + +# There are main objects, and their subclasses, here: +# LoadedForm +# DBHandler (generally referred to a an "upload handler", at present) +# DBConnector (UploadEngine) +# +# See their documentation below. + +# Write python 3 compatible code. +from __future__ import print_function +from __future__ import unicode_literals +from __future__ import absolute_import +from __future__ import division + +from csv import reader as csv_reader +from cgi import escape as cgi_escape +import collections +import ast +import markupsafe +import hashlib +import io + +# We are not really using wtforms. We use it to (barely) +# interact with the html and post request but really +# we define our own classes to handle working memory +# and interacting with the session. +from wtforms import ( + Form, + BooleanField, + StringField, + RadioField, + PasswordField, + FileField) + +import psycopg2 + +from pgwui_core.form_constants import * + + +# Setup default values for forms. + +class UserInitialPost(): + db = LIVE_DB + user = '' + password = '' + +class AuthInitialPost(): + db = '' + user = '' + password = '' + +class UploadFileInitialPost(AuthInitialPost): + upload_fmt = CSV + datafile = '' + trim_upload = True + +class UploadNullFileInitialPost(UploadFileInitialPost): + upload_null = True + null_rep = '' + +class UploadTableInitialPost(UploadNullFileInitialPost): + table = '' + +# The wtforms that suck data out of the html. + +class UserWTForm(Form): + '''The wtform used to connect to the db to authenticate .''' + # We don't actually use the labels, wanting the template to + # look (and render) like html, but I'll define them anyway + # just to keep my hand in. + user = StringField('User:') + password = PasswordField('Password:') + + ivals = UserInitialPost + + +class AuthWTForm(UserWTForm): + '''The wtform used to connect to any db and authenticate.''' + # We don't actually use the labels, wanting the template to + # look (and render) like html, but I'll define them anyway + # just to keep my hand in. + db = StringField('Database:') + + ivals = AuthInitialPost + + +class UploadFileWTForm(AuthWTForm): + '''The wtform used for uploading files.''' + # We don't actually use the labels, wanting the template to + # look (and render) like html, but I'll define them anyway + # just to keep my hand in. + upload_fmt = RadioField('Upload Format:', + choices=[('Upload CSV Data:', CSV), + ('Upload tab delimited Data:', TAB)]) + datafile = FileField('File with CSV or Tab delimited Data:') + trim_upload = BooleanField('Trim Leading/Trailing Spaces:') + + ivals = UploadFileInitialPost + + +class UploadNullFileWTForm(UploadFileWTForm): + '''The wtform used for uploading files that may contain NULL.''' + # We don't actually use the labels, wanting the template to + # look (and render) like html, but I'll define them anyway + # just to keep my hand in. + upload_null = BooleanField('Upload NULL Values:') + null_rep = StringField('NULL Representation:') + + ivals = UploadNullFileInitialPost + + +class UploadTableWTForm(UploadNullFileWTForm): + '''The wtform used for uploading arbitrary data into tables.''' + table = StringField('Table or View:') + + ivals = UploadTableInitialPost + + +class LoadedForm(collections.MutableMapping): + ''' + Abstract class representing an upload form. + + Responsible for getting information into and out of + html forms. + + The user API is that it acts like a dict, but with extra methods. + + Attributes: + uh The UploadHandler instance using the form + + _store Where the real dict is kept + _form Instantaiated html form object (WTForms) + _fc Class handling html form + ''' + def __init__(self, uh, fc=None, data={}, **kwargs): + super(LoadedForm, self).__init__() + self.uh = uh + if data == {}: + store = dict(kwargs) + else: + store = dict(data) + store.update(kwargs) + self._store = store + self._fc = fc + + def __iter__(self): return next(self._store) + def __len__(self): return len(self._store) + def __getitem__(self, key): return self._store[key] + def __setitem__(self, key, value): self._store[key] = value + def __delitem__(self, key): del self._store[key] + + def read(self): + ''' + In the children this loads form from pyramid self.uh.request + object and self._form and the session. + + In this case we instantiate _form and give it some defaults + ''' + self._form = self._fc(self.uh.request.POST, self._fc.ivals) + + def write(self, response, errors): + ''' + Produces the dict pyramid will use to render the form. + + Input: + response Dict of results from connection execution + errors List of errors from connection execution + ''' + response['errors'] = errors + return response + + +class CredsLoadedForm(LoadedForm): + ''' + Acts like a dict, but with extra methods. + Manages credentials (but not db) needed to authenticate. + + Attributes: + uh The UploadHandler instance using the form + user The username used to login + _form Instantaiated html form object (WXForms) + + Methods: + read() Load form from pyramid request object. + ''' + def __init__(self, uh, fc=UserWTForm, data={}, **kwargs): + data.update(kwargs) + super(CredsLoadedForm, self).__init__(uh, fc, data) + + def session_put(self, key, value): + ''' + Put data into the session. + + Input: + key The key + value The value + + Returns: + + Side effects: + Modifies session + + May be overridden by a subclass to keep data out + of the session. + ''' + self.uh.session[key] = value + + + def read(self): + ''' + Read form data from the client + ''' + + # Read parent's data + super(CredsLoadedForm, self).read() + + # Read our form data + + # Keep password and user in the session. All the other + # form varaibles must be re-posted. + post = self.uh.request.POST + session = self.uh.request.session + + # Defaults are now in place in self._form for password + # and user. Ignore these since we want to know whether + # to go to the session for data values. + if 'password' in post: + self['password'] = post['password'] + self.session_put('password', self['password']) + elif 'password' in session: + self['password'] = session['password'] + + if 'user' in post: + self['user'] = post['user'] + self.session_put('user', self['user']) + elif 'user' in session: + self['user'] = session['user'] + else: + self['user'] = '' + + # Other, hidden, POST variables + if 'action' in post: + self['action'] = post['action'] + else: + self['action'] = '' + + + def write(self, result, errors): + ''' + Produces the dict pyramid will use to render the form. + ''' + response = super(CredsLoadedForm, self).write(result, errors) + if ('havecreds' not in response + or ('havecreds' in response and not response['havecreds'])): + # We don't know if the credentials are good or + # we know they are bad. Keep them out of the session. + response['user'] = '' + response['password'] = '' + self.session_put('user', '') + self.session_put('password', '') + else: + response['user'] = self['user'] + return response + + +class AuthLoadedForm(CredsLoadedForm): + ''' + Acts like a dict, but with extra methods. + Manages form data needed to authenticate, including db to authenticate + in. + + Attributes: + uh The UploadHandler instance using the form + user The Usernamed used to login + db The db to login to + _form Instantaiated html form object (WXForms) + + ''' + def __init__(self, uh, fc=AuthWTForm, data={}, **kwargs): + data.update(kwargs) + super(AuthLoadedForm, self).__init__(uh, fc, data) + + def read(self): + ''' + Read form data from the client + ''' + + # Read parent's data + super(AuthLoadedForm, self).read() + + # Keep form variables handy + self['db'] = self._form.db.data + + + def write(self, result, errors): + ''' + Produces the dict pyramid will use to render the form. + ''' + response = super(AuthLoadedForm, self).write(result, errors) + response['db'] = self['db'] + return response + + +class UploadFileForm(AuthLoadedForm): + ''' + Acts like a dict, but with extra methods. + + Attributes: + uh The UploadHandler instance using the form + + Methods: + read() Load form from pyramid request object. + ''' + def __init__(self, uh, fc=UploadFileWTForm, data={}, **kwargs): + data.update(kwargs) + super(UploadFileForm, self).__init__(uh, fc, data) + + def read(self): + ''' + Read form data from the client + ''' + + # Read parent's data + super(UploadFileForm, self).read() + + # Read our own data + self['upload_fmt'] = self._form.upload_fmt.data + self['trim_upload'] = self._form.trim_upload.data + + # Other POST variables involving a file + self['filename'] = '' + self['localfh'] = '' + if 'action' in self: + if self._form.datafile.data != '': + post = self.uh.request.POST + if hasattr(post['datafile'], 'filename'): + self['filename'] = post['datafile'].filename + if hasattr(post['datafile'], 'file'): + self['localfh'] = post['datafile'].file + + + def write(self, result, errors): + ''' + Produces the dict pyramid will use to render the form. + ''' + if self['upload_fmt'] == CSV: + csv_checked = CHECKED + tab_checked = UNCHECKED + else: + tab_checked = CHECKED + csv_checked = UNCHECKED + + if self['trim_upload']: + trim_upload_checked = CHECKED + else: + trim_upload_checked = UNCHECKED + + response = super(UploadFileForm, self).write(result, errors) + response['filename'] = self['filename'] + response['trim_upload'] = trim_upload_checked + response['csv_value'] = CSV_VALUE + response['tab_value'] = TAB_VALUE + response['csv_checked'] = csv_checked + response['tab_checked'] = tab_checked + return response + + +class UploadDoubleFileForm(UploadFileForm): + ''' + Acts like a dict, but with extra methods. + + Attributes: + uh The UploadHandler instance using the form + + Methods: + read() Load form from pyramid request object. + ''' + def __init__(self, uh, fc=UploadFileWTForm, data={}, **kwargs): + data.update(kwargs) + super(UploadDoubleFileForm, self).__init__(uh, fc, data) + + def read(self): + ''' + Read form data from the client + ''' + # Read parent's data + super(UploadDoubleFileForm, self).read() + + # Read our own data + post = self.uh.request.POST + if 'last_key' in post: + self['last_key'] = post['last_key'] + else: + self['last_key'] = '' + + def write(self, result, errors): + ''' + Produces the dict pyramid will use to render the form. + ''' + response = super(UploadDoubleFileForm, self).write(result, errors) + response['last_key'] = self['last_key'] + return response + + +class UploadNullFileForm(UploadFileForm): + ''' + Acts like a dict, but with extra methods. + + Attributes: + uh The UploadHandler instance using the form + + Methods: + read() Load form from pyramid request object. + ''' + def __init__(self, uh, fc=UploadNullFileWTForm, data={}, **kwargs): + data.update(kwargs) + super(UploadNullFileForm, self).__init__(uh, fc, data) + + def read(self): + ''' + Read form data from the client + ''' + + # Read parent's data + super(UploadNullFileForm, self).read() + + # Read our own data + self['upload_null'] = self._form.upload_null.data + self['null_rep'] = self._form.null_rep.data + + + def write(self, result, errors): + ''' + Produces the dict pyramid will use to render the form. + ''' + if self['upload_null']: + upload_null_checked = CHECKED + else: + upload_null_checked = UNCHECKED + + response = super(UploadNullFileForm, self).write(result, errors) + response['upload_null'] = upload_null_checked + response['null_rep'] = self['null_rep'] + return response + + +class UploadTableForm(UploadNullFileForm): + ''' + Acts like a dict, but with extra methods. + + Attributes: + uh The UploadHandler instance using the form + + Methods: + read() Load form from pyramid request object. + ''' + def __init__(self, uh, fc=UploadTableWTForm, data={}, **kwargs): + data.update(kwargs) + super(UploadTableForm, self).__init__(uh, fc, data) + + def read(self): + ''' + Read form data from the client + ''' + + # Read parent's data + super(UploadTableForm, self).read() + + # Read our own data + self['table'] = self._form.table.data + + + def write(self, result, errors): + ''' + Produces the dict pyramid will use to render the form. + ''' + response = super(UploadTableForm, self).write(result, errors) + response['table'] = self['table'] + return response + + +class UploadDoubleTableForm(UploadTableForm): + ''' + Acts like a dict, but with extra methods. + + Attributes: + uh The UploadHandler instance using the form + + Methods: + read() Load form from pyramid request object. + ''' + def __init__(self, uh, fc=UploadTableWTForm, data={}, **kwargs): + data.update(kwargs) + super(UploadDoubleTableForm, self).__init__(uh, fc, data) + + def read(self): + ''' + Read form data from the client + ''' + # Read parent's data + super(UploadDoubleTableForm, self).read() + + # Read our own data + post = self.uh.request.POST + if 'last_key' in post: + self['last_key'] = post['last_key'] + else: + self['last_key'] = '' + + def write(self, result, errors): + ''' + Produces the dict pyramid will use to render the form. + ''' + response = super(UploadDoubleTableForm, self).write(result, errors) + response['last_key'] = self['last_key'] + return response + + +# Utility functions + +def textualize(st): + ''' + Return pg representation of NULL for None when string st is None. + ''' + return 'NULL' if st == None else st + +def is_checked(val): + '''Is the value something a html input entity recognizes as checked?''' + return val == CHECKED + +# Some functions for logging + +def escape_eol(string): + '''Change all the newlines to \n.''' + return string.replace('\n', r'\n') + +def format_exception(ex): + '''Return an exception formatted as suffix text for a log message.''' + if isinstance(ex, psycopg2.DatabaseError): + diag = ex.diag + msg = diag.message_primary + if hasattr(diag, 'message_detail'): + msg += ', detail={0}'.format(escape_eol(diag.message_detail)) + if hasattr(diag, 'message_hint'): + msg += ', hint={0}'.format(escape_eol(diag.message_hint)) + elif isinstance(ex, UploadError): + msg = ex.e + if ex.descr != '': + msg += ' {0}'.format(escape_eol(ex.descr)) + if ex.detail != '': + msg += ' {0}'.format(escape_eol(ex.detail)) + else: + msg = '' + if msg != '': + msg = ': Error is ({0})'.format(msg) + return msg + +# Error handling + +class UploadError(Exception): + ''' + Module exceptions are derived from this class. + + lineno Line number to which error pertains, if any + e The error message + descr More description of the error + detail Extra HTML describing the error + data Line of data causing problem, if any + + UploadError + * Error + * NoHeadersError + * NoDataError + * DBError + * DBCommitError + * DBDataLineError + * DataLineError + * TooManyColsError + ''' + def __init__(self, e, lineno = '', descr='', detail='', data = ''): + super(UploadError, self).__init__() + self.lineno = lineno + self.e = e + self.descr = descr + self.detail = detail + self.data = data + + def __str__(self): + out = 'error ({0})'.format(self.e) + if self.lineno != '': + out = '{0}: lineno ({1})'.format(out, self.lineno) + if self.descr != '': + out = '{0}: descr ({1})'.format(out, self.descr) + if self.detail != '': + out = '{0}: detail ({1})'.format(out, self.detail) + if self.data != '': + out = '{0}: data ({1})'.format(out, self.data) + return out + +class Error(UploadError): + ''' + Module exceptions rasied while setting up to read data lines + are derived from this class. + + e The error message + descr More description of the error + detail Extra HTML describing the error + ''' + def __init__(self, e, descr='', detail=''): + super(Error, self).__init__(e=e, descr=descr, detail=detail) + +class NoFileError(Error): + '''No file uploaded''' + def __init__(self, e, descr='', detail=''): + super(NoFileError, self).__init__(e, descr, detail) + +class NoDBError(Error): + '''No database name given''' + def __init__(self, e, descr='', detail=''): + super(NoDBError, self).__init__(e, descr, detail) + +class NoUserError(Error): + '''No user name supplied''' + def __init__(self, e, descr='', detail=''): + super(NoUserError, self).__init__(e, descr, detail) + +class AuthFailError(Error): + '''Unable to connect to the db''' + def __init__(self, e, descr='', detail=''): + super(AuthFailError, self).__init__(e, descr, detail) + +class DryRunError(Error): + '''Rollback due to dry_run config option''' + def __init__(self, e, descr='', detail=''): + super(DryRunError, self).__init__(e, descr, detail) + +class CSRFError(Error): + '''Invalid CSRF token''' + def __init__(self, e, descr='', detail=''): + super(CSRFError, self).__init__(e, descr, detail) + +class NoHeadersError(Error): + '''No column headings found''' + def __init__(self, e, descr='', detail=''): + super(NoHeadersError, self).__init__(e, descr, detail) + +class NoDataError(Error): + '''No data uploaded''' + def __init__(self, e, descr='', detail=''): + super(NoDataError, self).__init__(e, descr, detail) + +class DuplicateUploadError(Error): + '''The same filename updated twice into the same db''' + def __init__(self, e, descr='', detail=''): + super(DuplicateUploadError, self).__init__(e, descr, detail) + +class DataInconsistencyError(Error): + def __init__(self, e, descr='', detail=''): + super(DataInconsistencyError, self).__init__(e, descr, detail) + +class DBError(Error): + '''psycopg2 raised an error''' + def __init__(self, pgexc, e='process your request'): + ''' + pgexc The psycopg2 exception object + e Description of what PG was doing + ''' + super(DBError, self).__init__( + 'PostgreSQL is unable to ' + e + ':', + 'It reports:', + self.html_blockquote(pgexc)) + + def html_blockquote(self, ex): + ''' + Produce an html formatted message from a psycopg2 DatabaseError + exception. + ''' + primary = cgi_escape(ex.diag.message_primary) + + if ex.diag.message_detail == None: + detail = '' + else: + detail = '
DETAIL: ' + cgi_escape(ex.diag.message_detail) + + if ex.diag.message_hint == None: + hint = '' + else: + hint = '
HINT: ' + cgi_escape(ex.diag.message_hint) + + return '

{0}: {1}{2}{3}

'.format( + ex.diag.severity, + primary, + detail, + hint) + +class DBCommitError(DBError): + def __init__(self, pgexc): + super(DBCommitError, self).__init__(pgexc) + +class DBDataLineError(DBError): + '''Database generated an error while the processor was running.''' + + def __init__(self, udl, pgexc): + ''' + udl An UploadDataLine instance + pgexc The psycopg2 exception object + ''' + super(DBDataLineError, self).__init__(pgexc) + self.lineno = udl.lineno + self.data = udl.raw + + +class DataLineError(UploadError): + ''' + Module exceptions rasied while line-by-line processing the uploaded + data are derived from this class. + + lineno The line number + e The error message + descr More description of the error + detail Extra HTML describing the error + data The uploaded data + ''' + def __init__(self, lineno, e, descr='', detail='', data=''): + super(DataLineError, self).__init__(e, lineno, descr, detail, data) + +class TooManyColsError(DataLineError): + def __init__(self, lineno, e, descr='', detail='', data=''): + super(TooManyColsError, self).__init__(lineno, e, descr, detail, data) + + +# Upload processing + +class SQLCommand(object): + ''' + An SQL command that returns nothing + + Attributes: + stmt The statement, formatted for psycopg2 substitution + args Tuple of arguments used to substitute when executed. + ''' + def __init__(self, stmt, args, ec=None): + ''' + stmt The statement, formatted for psycopg2 substitution + args Tuple of arguments used to substitute when executed. + ec(ex) Produces the exception to raise an instance of on failure + Input: + ex The exception raised by psycopg2 + ''' + super(SQLCommand, self).__init__() + self.stmt = stmt + self.args = args + self.ec = ec + + + def execute(self, cur): + ''' + Execute the sql statement. + + Input: + cur A psycopg2 cursor + + Side effects: + Does something in the db. + Can raise a psycopg2 error + ''' + try: + cur.execute(self.stmt, self.args) + except psycopg2.DatabaseError as ex: + if self.ec == None: + raise ex + else: + raise self.ec(ex) + + +class LogSQLCommand(SQLCommand): + '''An SQL command that logs success or failure.''' + def __init__(self, stmt, args, ec=None, + log_success=None, log_failure=None): + ''' + stmt The statement, formatted for psycopg2 substitution + args Tuple of arguments used to substitute when executed. + ec(ex) Produces the exception to raise an instance of on failure + Input: + ex The exception raised by psycopg2 + ''' + super(LogSQLCommand, self).__init__(stmt, args, ec) + self.log_success = log_success + self.log_failure = log_failure + + def execute(self, cur): + ''' + Execute the sql statement. + + Input: + cur A psycopg2 cursor + + Side effects: + Does something in the db. + Can raise a psycopg2 error + ''' + try: + super(LogSQLCommand, self).execute(cur) + except (UploadError, psycopg2.DatabaseError) as ex: + if self.log_failure: + self.log_failure(ex) + raise + else: + if self.log_success: + self.log_success() + + +class UploadLine(object): + ''' + Representation of a generic uploaded line + + Responsbile for getting data out of uploaded lines. + + Once out, the following attributes provide the user API: + raw The "raw" line as a string + tuples A sequence, the line split into columns + ''' + def __init__(self, line, stol, mapper): + ''' + line Uploaded line + lineno Line number + stol(st) Parse string st and convert into list + mapper(st) Maps st onto desired python representation + (Used for trimming whitespace) + ''' + super(UploadLine, self).__init__() + self.raw = line + self.tuples = [mapper(st) for st in stol(line)] + +def doublequote(st): + ''' + Put string in double quotes escaping according to sql's + requirements for an identifier. + + Note that this does not work for unicode identifiers. + ''' + out = '"' + for ch in st: + if ch == '"': + out += '""' + else: + out += ch + return out + '"' + +class UploadHeaders(UploadLine): + '''Uploaded heading line + + Derived from UploadLine + + raw The "raw" line as a string + tuples As a sequence + sql As a sql command fragment string + ''' + + def __init__(self, line, stol, mapper): + + if mapper(line) == '': + raise NoHeadersError('No column headings found on first line', + 'The first line is ({0})'.format(line)) + + super(UploadHeaders, self).__init__(line, stol, mapper) + self.sql = ', '.join(['"' + doublequote(st) + '"' + for st in self.tuples]) + + +class UploadDataLine(UploadLine): + '''Uploaded data line + + Derived from UploadLine + + raw The "raw" line as a string + tuples As a sequence + lineno The line number + ''' + def __init__(self, line, lineno, stol, mapper): + super(UploadDataLine, self).__init__(line, stol, mapper) + self.lineno = lineno + + +class DBData(object): + '''Data that is to modify the db. + + It is iterable, consisting of thunks which make an UploadedLine instance. + + lineno Number of lines processed (including header line) + + ''' + def __init__(self): + self.lineno = 0 + + def __iter__(self): + return self + + def __next__(self): + ''' + Iterator to return a thunk which, when called, delivers the + next object to be loaded into the db.''' + self.lineno += 1 + return self._thunk() + + def _thunk(): + ''' + Return a thunk which, when called, delivers the next + object to go into the db. + ''' + raise NotImpementedError() + + +class SQLData(DBData): + ''' + SQL statements returning no data that execute in the db. + + Attributes: + stmts List of SQLCommand instances + ''' + def __init__(self, stmts): + ''' + stmts List of SQLCommand instances + ''' + super(SQLData,self).__init__() + self.stmts = stmts + + def gen(stmts): + for stmt in stmts: + yield stmt + + self.stmt_gen = gen(stmts) + + def _thunk(self): + stmt = next(self.stmt_gen) + return lambda: stmt + + +class UploadData(DBData): + '''Uploaded data file + + It is iterable, consisting of thunks which make an UploadedLine instance. + + headers UploadedHeaders instance + cols Number of columns + lineno Number of lines processed (including header line) + + ''' + def __init__(self, fileo, file_fmt, null_data, null_rep, trim=True): + ''' + fileo Uploaded file object + file_fmt File format: CSV or TAB + null_data (boolean) Uploaded data contains nulls + null_rep Uploaded string representation of null + trim (boolean) Trim leading and trailing whitespace? + ''' + + def get_headers(): + try: + line = next(self._fileo) + except StopIteration: + raise NoDataError('Uploaded file contains no data') + else: + self.lineno += 1 + # Intuit the eol sequence + if line[-2:] == '\r\n': + eol = '\r\n'; + line = line[:-2] + elif line[-1:] == '\n': + eol = '\n' + line = line[:-1] + elif line[-1:] == '\r': + eol = '\r' + line = line[:-1] + else: + # Give up + eol = '' + + if file_fmt == CSV: + func = lambda st: next(csv_reader((st,))) + else: + func = lambda st: st.split('\t') + return (eol, UploadHeaders(line, func, do_trim)) + + super(UploadData, self).__init__() + + if trim: + do_trim = lambda st: st.strip() + else: + do_trim = lambda st: st + + # Read lines as text with line endings intact. + # newline='' required by csv.reader() + self._fileo = io.TextIOWrapper(fileo, newline='') + + # Get column headings + eol, self.headers = get_headers() + neg_eollen = -len(eol) + self.cols = len(self.headers.tuples) + + # Create parser to read raw lines into a list + if file_fmt == CSV: + self._parser = lambda st: self._extend(st, + next(csv_reader((st,)))) + else: # Tab delimited format + def tab_parser(line): + if neg_eollen and line[neg_eollen:] == eol: + line = line[:neg_eollen] + return self._extend(line, line.split('\t')) + self._parser = tab_parser + + # Create mapper to frob data elements + if null_data: + null_rep = do_trim(null_rep) + # psycopg2 maps None to NULL + def mapper(st): + st = do_trim(st) + return None if st == null_rep else st + self._mapper = mapper + else: + self._mapper = do_trim + + def _thunk(self): + ''' + Return a thunk which, when called, delivers the + UploadDataLine of the next line of the uploaded file.. + ''' + line = next(self._fileo) + return lambda: UploadDataLine(line, + self.lineno, + self._parser, + self._mapper) + + def _extend(self, line, seq): + '''Give the list as many elements as there are in the header. + + line line as string + seq line as sequence + + If there's too many elements, raise an error. + ''' + if len(seq) > self.cols: + raise TooManyColsError(self.lineno, + 'Line has too many columns', + 'More columns than column headings', + data=line) + return seq + [ '' for i in range(len(seq)+1, self.cols)] + + + +class DataLineProcessor(object): + ''' + A processor supplied uploaded lines (UploadDataLine instances) + by an UploadEngine. The lines are expected to be put into a pg db. + + Abstract class not expected to be instantiated. + + Attributes: + ue UploadEngine instance + uh UploadHandler instance + cur psycopg2 cursor + + Methods: + eat(udl) Given an UploadDataLine instance put the line in the db. + ''' + def __init__(self, ue, uh): + ''' + ue UploadEngine instance + uh UploadHandler instance + ''' + super(DataLineProcessor, self).__init__() + self.ue = ue + self.uh = uh + self.cur = ue.cur + + def eat(udl): + ''' + Update the db with the content of an uploaded line + + udl An UploadDataLine instance + ''' + raise NotImplementedError + + +class NoOpProcessor(DataLineProcessor): + '''A processor that discards it's input.''' + def __init__(self, ue, uh): + ''' + ue UploadEngine instance + uh UploadHandler instance + cur psycopg2 cursor + ''' + super(NoOpProcessor, self).__init__(ue, uh) + + + def eat(self, udl): + ''' + Executes an sql command in the db. + + udl A DataLine instance. + ''' + pass + + +class ExecuteSQL(DataLineProcessor): + def __init__(self, ue, uh): + ''' + ue UploadEngine instance + uh UploadHandler instance + cur psycopg2 cursor + ''' + super(ExecuteSQL, self).__init__(ue, uh) + + + def eat(self, sqlc): + ''' + Executes an sql command in the db. + + sqlc An SQLCommand instance (a command and it's args) + ''' + sqlc.execute(self.cur) + + +class DBHandler(object): + ''' + Abstract class of a handler that modifies the db. + + The main logic goes here, including getting the data + into and out of the db. + + Responsible for: + Telling the form (LoadedForm) to get user data + Retrieval of data file or generation of other data to go in the db + (Generally involving an UploadData instance, and hence an UploadLine + instance.) + Validation of user supplied data; error raising: + The html form data + Whatever other data is uploaded or otherwise passed in + Pre-processing to prepare for getting data into the db + (Pre-processing is referred to as "setup" presently.) + Getting the individual bits of data into and out of the db + (by way of having a factory that produces a DataLineProcessor) + Post-processing to wrap up after the data is in the db + (Post-processing is referred to as "cleanup" presently.) + Rendering the html output + + Attributes: + request A pyramid request instance + uf An UploadForm instance + data Something (beyond what's on the form) that goes into db + ''' + def __init__(self, request): + ''' + request A pyramid request instance + ''' + super(DBHandler, self).__init__() + self.request = request + self.uf = self.make_form() + + def make_form(self): + ''' + Return an instantiation of the upload form needed + by the upload handler. + ''' + raise NotImpliementedError + + def get_data(self): + ''' + Put something that will go into the db into the 'data' attribute. + ''' + raise NotImplimentedError + + def val_input(self): + ''' + Validate input needed beyond that required to connect to the db. + + Note that this occurs after read() is called. + + This is expected to be replaced by it's subclass. + ''' + return [] + + def read(self): + '''Read the html form into the upload form instance''' + self.uf.read() + + def write(self, result, errors): + ''' + Return dict needed to render an html form + + Input: + errors List of Error instances + + Returns: + Dict pyramid will use to render the resulting form + Reserved keys: + errors A list of UploadError exceptions. + ''' + return self.uf.write(result, errors) + + def cleanup(self): + ''' + Called after all lines are processed to do any final + updates to the db. + ''' + pass + + def render(self, errors, response): + ''' + Return to pyramid what's needed to render the appropriate html + page. + + Input: + errors List of Error instances + response Db connection result dict + + Returns: + Dict pyramid will use to render the resulting form + ''' + response = self.write(response, errors) + return response + + +class SessionDBHandler(DBHandler): + ''' + A DBHandler that supports sessions. + + Attributes: + uf An UploadForm instance + session A pyramid session instance + ''' + def __init__(self, request): + ''' + request A pyramid request instance + ''' + super(SessionDBHandler, self).__init__(request) + self.session = self.request.session + + def write(self, result, errors): + ''' + Add csrf token into html form to protect sessions. + + Input: + errors List of Error instances + + Returns: + Dict pyramid will use to render the resulting form + Reserved keys: + errors A list of UploadError exceptions. + csrf_token Token for detecting CSRF. + ''' + response = super(SessionDBHandler, self).write(result, errors) + response['csrf_token'] = self.session.new_csrf_token() + return response + + +class UploadHandler(SessionDBHandler): + ''' + Handler for uploading a file. + + Attributes: + request A pyramid request instance + uf An UploadForm instance + data (optional) A DBData instance + ''' + def __init__(self, request): + ''' + request A pyramid request instance + ''' + super(UploadHandler, self).__init__(request) + + def factory(self, ue): + ''' + Takes an UploadEngine instance + Returns a DataLineProcessor instance + ''' + raise NotImplementedError + + def val_input(self): + ''' + Validate input needed beyond that required to connect to the db. + + Returns: + A list of Error instances + ''' + uf = self.uf + errors = super(UploadHandler, self).val_input() + + if uf['filename'] == '': + errors.append(NoFileError('No file supplied')) + + return errors + + def double_validator(self, errors): + '''Utility function that can optionally be called by + a val_input() function. It checks that the same file + has not been uploaded twice in succession to the same + db. + + `errors` + List of errors. Appended to. + ''' + uf = self.uf + if self.make_double_key() == uf['last_key']: + errors.append(DuplicateUploadError( + 'File just uploaded to this db', + ('File named ({0}) just uploaded' + .format(markupsafe.escape(uf['filename']))), + '

Try again to force upload.

')) + + def hash_sequence(self, seq): + '''Produce a hash of the elements of a sequence.''' + hash = hashlib.md5() + for item in seq: + hash.update((hash.hexdigest() + item).encode('utf-8')) + return hash.hexdigest() + + def make_double_key(self): + '''Generate unique value which identifies a double upload.''' + uf = self.uf + return self.hash_sequence((uf['db'], uf['filename'])) + + def write_double_key(self, response): + '''Utility function. Optionally called from within write() + to save a key which is later tested for to determine if + the same file is being uploaded twice in a row. + + This function keys by filename and db. + + The key is stored in the form and submitted in POST. + This way if the session times out due to inactivity + the double upload is still detected. + + Since the data is delivered to the client and the + client will likely see it anyway we use a hash not + for security but just to provide a convenient single + value that can be tested. + + Input: + response Dict used by pyramid to render html form. + + Side effects: + Modifies response. Adds 'last_key' entry used by form to store key. + ''' + response['last_key'] = self.make_double_key() + + def write(self, result, errors): + ''' + Add lines processed and number of errors into html form + shown the user. + + Input: + errors List of Error instances + + Returns: + Dict pyramid will use to render the resulting form + Reserved keys: + errors A list of UploadError exceptions. + csrf_token Token for detecting CSRF. + e_cnt Number of errors. + db_changed Boolean. Whether the db was changed. + ''' + response = super(UploadHandler, self).write(result, errors) + if hasattr(self, 'data'): + response['lines'] = self.data.lineno - 1 + response['e_cnt'] = len(errors) + response['db_changed'] = (not response['errors'] + and self.uf['action'] != '') + return response + + +class TabularFileUploadHandler(UploadHandler): + ''' + Handler for uploading a file with rows and columns and column headings. + + Attributes: + request A pyramid request instance + uf An UploadForm instance + data An UploadData instance + ''' + def __init__(self, request): + ''' + request A pyramid request instance + ''' + super(TabularFileUploadHandler, self).__init__(request) + + def cleanup(self): + '''Finish after processing all lines.''' + lines = self.ue.data.lineno + if lines == 1: + raise DataLineError( + 1, + 'File contains no data', + ('No lines found after ' + 'initial line of column headings')) + + +class DBConnector(object): + '''Abstract class supporting db connection and execution of a + processor function that alters the db content. + + Responsible for connecting to the db, transaction management, + and running the DataLineProcessor instances produced by the + DBConnector's (the UploadHandler's) factory. + Collects all errors raised during the processing. + Telling the uploadhandler to cleanup. This is done after + all upload processing and before commit or rollback + (and before the connection is closed). + + Attributes: + uh An UploadHandler instance. + cur A psycopg2 cursor instance + db Name of db to connect to + user User to connect to db + password Password to connect to db + action Upload form's hidden action variable + '' means not submitted, anything else means take action + + Methods: + run() Get a DataLineProcessor instance from the upload handler's + factory and feed it by iterating over data. + ''' + + def __init__(self, uh): + ''' + uh An UploadHandler instance + ''' + super(DBConnector, self).__init__() + + # Configuration and response management. + self.uh = uh + + def alter_db(self, conn): + ''' + Alter the contents of the db. + + Input: + conn A database connection + + Returns: + A list of Error instances + + Side Effects: + Alter's db + ''' + + raise NotImplementedError + + + def no_connection_response(self): + ''' + The result dict to use when call_with_connection is not called. + Matches with the result dict of call_with_connection + + Returns: + Dict pyramid will use to render the resulting form. + Reserved keys: + havecreds Boolean. Supplied credentials can connect to db. + ''' + return {'havecreds' : False} + + def nodberror_factory(self): + return NoDBError('No database name supplied') + + def nousererror_factory(self): + return NoUserError('No user name supplied as login credentials') + + def authfailerror_factory(self): + return AuthFailError('Unable to login', + 'Is the database, user, and password correct?') + + def dryrunerror_factory(self): + return DryRunError('Configured for "dry_run":' + ' Transaction deliberately rolled back') + + def upload_data(self, data, errors): + '''Put a DBData object into the db. + + Input: + data A DBData object. + errors A list of errors + + Side Effects: + Alters db content + Add errors to `errors`. + ''' + raise NotImplementedError + + def alter_db(self, conn): + ''' + Alter the contents of the db. + + Input: + conn A database connection + + Returns: + A list of Error instances + + Side Effects: + Alter's db + ''' + + errors = [] + try: + self.uh.get_data() + self.data = self.uh.data + self.cur = conn.cursor() + # (Cannot call uh until after self is fully + # initalized, including self.cur.) + processor = self.uh.factory(self) + except Error as ex: + errors.append(ex) + else: + try: + self.upload_data(processor, self.data, errors) + # Let upload handler finish + try: + self.uh.cleanup() + except UploadError as ex: + errors.append(ex) + finally: + self.cur.close() + return errors + + def call_with_connection(self, func): + ''' + Validate input, connect to the db, and do something with + the connection. + + func(conn) Call this function with the connection. + func(conn) must return a list of Error instances + + Returns: + (errors, response) + errors List of Error instances + response Dict pyramid will use to render the resulting form. + The dict returned by func(conn) plus reserved keys. + Reserved keys: + havecreds Boolean. Supplied credentials can + connect to db. + Side effects: + Raises errors, calls func(conn) + ''' + errors = [] + havecreds = False + response = {} + + uf = self.uh.uf + + if self.db == '': + errors.append(self.nodberror_factory()) + + if self.user == '': + errors.append(self.nousererror_factory()) + + newes = self.uh.val_input() + if newes: + if not errors: + havecreds = True + errors.extend(newes) + + if not errors: + registry = self.uh.request.registry + try: + conn = psycopg2.connect( + database = self.db, + user = self.user, + password = self.password, + host = registry.settings['pg_host'], + port = registry.settings['pg_port']) + except psycopg2.OperationalError: + errors = [self.authfailerror_factory()] + havecreds = False + else: + havecreds = True + errors = self.call_alter_db(func, conn) + + response.update({'havecreds' : havecreds + }) + return (errors, response) + + def read_uh(self): + '''Read data into the upload handler.''' + self.uh.read() + + def read_db(self): + '''Read the db from the upload handler.''' + self.db = self.uh.uf['db'] + + def read_user(self): + '''Read the username from the upload handler.''' + self.user = self.uh.uf['user'] + + def read_password(self): + '''Read the password from the upload handler.''' + if 'password' in self.uh.uf: + self.password = self.uh.uf['password'] + else: + self.password = '' + + def read_action(self): + '''Read the action from the upload handler.''' + self.action = self.uh.uf['action'] + + def read(self): + '''Allows for custom engines to map what the handler + has to what they need. + ''' + self.read_uh() + self.read_db() + self.read_user() + self.read_password() + self.read_action() + + def run(self): + '''Call the alter_db function with the connection to alter the db, + render form and return Response + + Input: + + Returns: + (errors, response) + errors List of Error instantiations + response Dict containing connection result info + + Side effects: + Maintains session + (Whatever the processor() call does) + Outputs html + ''' + self.read() + + if self.action == 'u': + errors, response = self.call_with_connection(self.alter_db) + else: + errors = [] + response = self.no_connection_response() + + return self.uh.render(errors, response) + + +class NoTransactionEngine(DBConnector): + '''An engine that does not run things in a transaction. + + It also does not do CSRF checking. + + Attributes: + uh An UploadHandler instance. + data An UploadData instance of the uploaded data + cur A psycopg2 cursor instance + db Name of db to connect to + user User to connect to db + password Password to connect to db + action Upload form's hidden action variable + '' means not submitted, anything else means take action + + Methods: + run() Get a DataLineProcessor instance from the upload handler's + factory and feed it by iterating over data. + ''' + def __init__(self, uh): + ''' + uh An UploadHandler instance + ''' + super(NoTransactionEngine, self).__init__(uh) + + def call_alter_db(self, func, conn): + ''' + Call a database modification function with a db connection, + turning off the automatic wrapping of the activity in + a transaction. + + func(conn) Call this function with the connection. + func(conn) must return a list of Error instances + + Returns: + errors List of Error instances + Side effects: + Calls func(conn) + ''' + conn.set_session(autocommit=True) + errors = func(conn) + conn.close() + return errors + + def upload_data(self, processor, data, errors): + '''Put a DBData object into the db, without a wrapping transaction. + + Input: + processor A DataLineProcessor object. + data A DBData object. + errors A list of errors + + Side Effects: + Alters db content + Add errors to `errors`. + ''' + for thunk in data: + try: + udl = thunk() + except DataLineError as ex: + errors.append(ex) + else: + try: + processor.eat(udl) + except psycopg2.DatabaseError as ex: + errors.append(DBDataLineError(udl, ex)) + except DataLineError as ex: + errors.append(ex) + except DBError as ex: + errors.append(ex) + + +class UnsafeUploadEngine(DBConnector): + '''Abstract class supporting repeatedly running a processer to put + uploaded data into db. + + Attributes: + uh An UploadHandler instance. + data An UploadData instance of the uploaded data + cur A psycopg2 cursor instance + db Name of db to connect to + user User to connect to db + password Password to connect to db + action Upload form's hidden action variable + '' means not submitted, anything else means take action + + Methods: + run() Get a DataLineProcessor instance from the upload handler's + factory and feed it by iterating over data. + eat_old_line(udl, thunk) + Trap errors raised by the db while running thunk. + Report any errors as due to the udl UploadDataLine + instance. + ''' + def __init__(self, uh): + ''' + uh An UploadHandler instance + ''' + super(UnsafeUploadEngine, self).__init__(uh) + + def call_alter_db(self, func, conn): + ''' + Call a database modification function with a connection. + + func(conn) Call this function with the connection. + func(conn) must return a list of Error instances + + Returns: + errors List of Error instances + Side effects: + Calls func(conn) + ''' + errors = func(conn) + + if errors: + conn.rollback() + else: + if ast.literal_eval(self.uh.request.registry.settings['dry_run']): + conn.rollback() + errors.append(self.dryrunerror_factory()) + else: + try: + conn.commit() + except psycopg2.DatabaseError as ex: + errors.append(DBCommitError(ex)) + conn.close() + return errors + + def eat_old_line(self, udl, thunk): + ''' + Run thunk and report any errors raised by the db as due to + the UploadDataLine instance udl. + + Returns: + The result of running thunk. + ''' + try: + result = thunk() + except psycopg2.DatabaseError as ex: + raise DBDataLineError(udl, ex) + else: + return result + + def upload_data(self, processor, data, errors): + '''Put a DBData object into the db. + + Input: + processor A DataLineProcessor object. + data A DBData object. + errors A list of errors + + Side Effects: + Alters db content + Add errors to `errors`. + ''' + for thunk in data: + try: + udl = thunk() + except DataLineError as ex: + errors.append(ex) + else: + self.cur.execute( + 'SAVEPOINT line_savepoint;') + try: + processor.eat(udl) + except psycopg2.DatabaseError as ex: + self.cur.execute( + 'ROLLBACK TO line_savepoint;') + errors.append(DBDataLineError(udl, ex)) + except DataLineError as ex: + self.cur.execute( + 'ROLLBACK TO line_savepoint;') + errors.append(ex) + except DBError as ex: + self.cur.execute( + 'ROLLBACK TO line_savepoint;') + errors.append(ex) + else: + self.cur.execute( + 'RELEASE line_savepoint;') + + +class UploadEngine(UnsafeUploadEngine): + '''Abstract class supporting repeatedly running a processor + to alter db content. Adds cross-site request forgery checking + to the UnsafeUploadEngine class. + + Attributes: + uh An UploadHandler instance. + cur A psycopg2 cursor instance + db Name of db to connect to + user User to connect to db + password Password to connect to db + action Upload form's hidden action variable + '' means not submitted, anything else means take action + csrf_token The client's csrf_token + + Methods: + run() Get a DataLineProcessor instance from the upload handler's + factory and feed it by iterating over data. + ''' + + def __init__(self, uh): + ''' + uh An UploadHandler instance + ''' + super(UploadEngine, self).__init__(uh) + + def csrferror_factory(self): + return CSRFError( + 'Your request failed and you are now logged out', + ('This is a security measure. ' + 'Some possible causes are:'), + ('
    ' + '
  • Cookies are off in the browser
    • ' + '
  • Reload of an expired page
    • ' + '
      ' + '
    • Use of the Back button to (re)submit' + ' an old page
      • ' + '
    • An attacker has crafted a page which resubmits' + ' one of your old page submissions
      • ' + '
    ' + '
  • Server restart
    • ' + '
  • Login session expired due to inactivity
    • ' + '
')) + + def read_csrf_token(self): + '''Save the csrf token.''' + post = self.uh.request.POST + if 'csrf_token' in post: + self.csrf_token = post['csrf_token'] + else: + self.csrf_token = None + + def read(self): + '''Add a csrf_token.''' + super(UploadEngine, self).read() + self.read_csrf_token() + + def call_with_connection(self, func): + ''' + Connect to the db. + + func(conn) Call this function with the connection. + f(conn) must return a (errors, dict) tuple result, + errors list of Error instances + dict other results + + Returns: + (errors, response) + errors List of Error instances + response Dict pyramid will use to render the resulting form. + The dict returned by func(conn) plus reserved keys. + Reserved keys: + havecreds Boolean. Supplied credentials can + connect to db. + session_expired Boolean. Session expired. + Side effects: + Raises errors, calls func(conn) + ''' + session = self.uh.session + + token = session.get_csrf_token() + if token != self.csrf_token: + session.invalidate() + response = self.no_connection_response() + response['session_expired'] = True + return([self.csrferror_factory()] + , response) + else: + (errors, response) = (super(UploadEngine, self) + .call_with_connection(func)) + response['session_expired'] = False + return (errors, response) diff --git a/tests/test_pgwui_core.py b/tests/test_pgwui_core.py new file mode 100644 index 0000000..3508284 --- /dev/null +++ b/tests/test_pgwui_core.py @@ -0,0 +1,29 @@ +# Copyright (C) 2018 The Meme Factory, Inc. http://www.meme.com/ + +# This file is part of PGWUI_Core. +# +# This program is free software: you can redistribute it and/or +# modify it under the terms of the GNU Affero General Public License +# as published by the Free Software Foundation, either version 3 of +# the License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU +# Affero General Public License for more details. +# +# You should have received a copy of the GNU Affero General Public +# License along with this program. If not, see +# . +# + +# Karl O. Pinc + +from pgwui_core import pgwui_core +import pgwui_core.form_constants import * + +def test_userinitialpost_init(): + uip = pgwui_core.UserInitialPost() + assert uip.db == LIVE_DB + assert uip.user == '' + assert uip.password == '' diff --git a/tox.ini b/tox.ini new file mode 100644 index 0000000..756fce9 --- /dev/null +++ b/tox.ini @@ -0,0 +1,27 @@ +[tox] +envlist = py{34,35,36,37} + +[testenv] +basepython = + py34: python3.4 + py35: python3.5 + py36: python3.6 + py37: python3.7 +deps = + check-manifest + {py34,py35,py36,py37}: readme_renderer + flake8 + pytest + pytest-cov + # coverage +commands = + check-manifest + {py34,py35,py36,py37}: python setup.py check -m -r -s + flake8 . + py.test --cov=pgwui_core tests/ + # coverage run --source src/pgwui_core -m py.test + # coverage report + +[flake8] +exclude = .tox,*.egg,build,data,devel +select = E,W,F